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- PDB-5yjw: Structure of the Ndi1 protein from Saccharomyces cerevisiae in co... -

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Basic information

Entry
Database: PDB / ID: 5yjw
TitleStructure of the Ndi1 protein from Saccharomyces cerevisiae in complex with the competitive inhibitor, stigmatellin.
ComponentsRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
KeywordsOXIDOREDUCTASE / monotopic membrane protein / NUCLEOTIDE-BINDING DOMAIN
Function / homology
Function and homology information


NADH:quinone reductase (non-electrogenic) / NADH oxidation / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / positive regulation of apoptotic process / mitochondrion / identical protein binding
Similarity search - Function
Alternative NADH dehydrogenase / FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / STIGMATELLIN A / Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYamasita, T. / Inaoka, D.K. / Shiba, T. / Oohashi, T. / Iwata, S. / Yagi, T. / Kosaka, H. / Harada, S. / Kita, K. / Hirano, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHI15K07005 Japan
CitationJournal: Sci Rep / Year: 2018
Title: Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors
Authors: Yamashita, T. / Inaoka, D.K. / Shiba, T. / Oohashi, T. / Iwata, S. / Yagi, T. / Kosaka, H. / Miyoshi, H. / Harada, S. / Kita, K. / Hirano, K.
History
DepositionOct 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,81927
Polymers54,0781
Non-polymers4,74126
Water6,215345
1
A: Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
hetero molecules

A: Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,63854
Polymers108,1562
Non-polymers9,48352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area17620 Å2
ΔGint-77 kcal/mol
Surface area43020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.670, 128.456, 86.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-805-

HOH

21A-992-

HOH

31A-1038-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial / Internal NADH dehydrogenase / NADH:ubiquinone reductase (non-electrogenic)


Mass: 54077.922 Da / Num. of mol.: 1 / Fragment: UNP residues 30-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NDI1, YML120C, YM7056.06C / Production host: Escherichia coli (E. coli)
References: UniProt: P32340, NADH:quinone reductase (non-electrogenic)

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Non-polymers , 11 types, 371 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H42O7
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM Mes(pH 6.0), 34%(v/v) PEG 400, 100mM NaCl, 2% (v/v) ethylene glycol, 5%(v/v) glycerol
PH range: 6.0-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 28, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 49022 / % possible obs: 99.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G9K

4g9k


Resolution: 1.85→29.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.811 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 2632 5.1 %RANDOM
Rwork0.18227 ---
obs0.18341 49008 92.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.04 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.85→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 317 345 4240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024132
X-RAY DIFFRACTIONr_bond_other_d0.0040.024088
X-RAY DIFFRACTIONr_angle_refined_deg1.4432.0435555
X-RAY DIFFRACTIONr_angle_other_deg1.1213.0079439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6265477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08924.037161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42615676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.51520
X-RAY DIFFRACTIONr_chiral_restr0.0690.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214409
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02890
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9142.0641881
X-RAY DIFFRACTIONr_mcbond_other0.9142.0641880
X-RAY DIFFRACTIONr_mcangle_it1.6263.0862367
X-RAY DIFFRACTIONr_mcangle_other1.6263.0862368
X-RAY DIFFRACTIONr_scbond_it1.0432.5572251
X-RAY DIFFRACTIONr_scbond_other1.0432.5582252
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7893.6693189
X-RAY DIFFRACTIONr_long_range_B_refined5.67119.174872
X-RAY DIFFRACTIONr_long_range_B_other5.38918.7754748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 85 -
Rwork0.24 1920 -
obs--49.52 %

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